Difference between revisions of "Team:Sydney Australia/Hexagon"

 
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{{:Team:Sydney_Australia/Templates/NavBar}}
 
 
<html>
 
<html>
 
<head>
 
<head>
 +
<script src="https://2017.igem.org/Team:Sydney_Australia/Resources/angularplasmid.complete.min.js"></script>
 +
<script src="http://code.jquery.com/jquery-2.1.0.min.js"></script>
 +
<link href="https://fonts.googleapis.com/css?family=Quicksand:300,400|Roboto:400,400i" rel="stylesheet">
 +
 +
<script type="text/javascript" src="https://use.fontawesome.com/2967839f93.js"></script>
 +
<meta name="viewport" content="width=device-width, initial-scale=1">
 +
  <link href="https://fonts.googleapis.com/css?family=Quicksand" rel="stylesheet">
 +
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
  
 
<script>
 
<script>
 +
$(document).ready(function() {
 +
  $(function() {
 +
      $('#pip').click(function() {
 +
          $('.pip_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#boriv').click(function() {
 +
          $('.boriv_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#eoriv').click(function() {
 +
          $('.eoriv_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#mcs1').click(function() {
 +
          $('.mcs_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#mcs2').click(function() {
 +
          $('.mcs_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#anti').click(function() {
 +
          $('.anti_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#super').click(function() {
 +
          $('.super_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#lacr').click(function() {
 +
          $('.lacr_info').fadeToggle('slow');
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.laco_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
  $(function() {
 +
      $('#laco').click(function() {
 +
          $('.laco_info').fadeToggle('slow');
 +
          $('.lacr_info').hide();
 +
          $('.pip_info').hide();
 +
          $('.eoriv_info').hide();
 +
          $('.boriv_info').hide();
 +
          $('.mcs_info').hide();
 +
          $('.anti_info').hide();
 +
          $('.super_info').hide();             
 +
      });       
 +
  });
 +
 +
  });
 
</script>
 
</script>
 
<style>
 
<style>
−
 
+
  .plasmid .markerhover:hover {
−
.arrow-right {
+
   stroke: #e2e2e2;
−
   width: 0;  
+
   stroke-width: 2px;
−
   height: 0;
+
−
  border-top: 40px solid transparent;
+
−
  border-bottom: 40px solid transparent;
+
−
  position:relative;
+
−
  bottom:15px;
+
−
 
+
−
 
+
 
}
 
}
−
.yncm-arrow {border-left: 40px solid #fadda2;}
+
  .plasmid .track {
−
.his-arrow {border-left: 40px solid #a396c6;}
+
  fill: #cfd9db;
−
.tev-arrow {border-left: 40px solid #f1ccf0;}
+
  stroke: #c0cdd1;
−
.winsulin-arrow {border-left: 40px solid #b0dfb3;}
+
−
 
+
−
.construct:after {
+
−
margin-top:150px;margin-left:10%;margin-right:10%;
+
−
position: absolute; 
+
−
display: inline-block;
+
−
bottom:53px;
+
−
left:0;
+
−
right:0;
+
−
height: 3px;
+
−
content: '';
+
−
background-color: #3e3f3f;
+
−
z-index:-1;
+
 
}
 
}
−
.element {
+
  .plasmid .tracklabelbody {
−
height:50px;
+
  font: 400 20px "Quicksand";
−
display:inline-block;
+
  fill: #5e7980;
−
text-align: center;
+
}
−
vertical-align: middle;
+
  .plasmid .tracklabeltitle {
−
line-height: 50px;  
+
  font: 700 40px "Quicksand";
−
font-family:'Quicksand' ;
+
  fill: #334145;
−
font-size:1.3vw;
+
}
−
color:#3e3f3f;  
+
  .plasmid .tracklabelsmall {
 +
  font: 400 12px "Quicksand";
 +
  fill: #5e7980;
 +
}
 +
  .plasmid .scale-major {
 +
  stroke: #334145;
 +
  stroke-width: 2px;
 +
}
 +
  .plasmid .scale-minor {
 +
  stroke: #94aab0;
 +
}
 +
  .plasmid .scale-majortext {
 +
  font: 300 9px "Quicksand";
 +
  fill: #94aab0;
 +
}
 +
  .plasmid .markerlabel {
 +
  font: 400 9px "Quicksand";
 +
  fill: #334145;
 +
}
 +
  .plasmid .featurelabel {
 +
  font: 700 14px "Quicksand";
 +
  fill: #c00;
 +
}
 +
  .plasmid .regionlabel {
 +
  font: 400 11px "Lato";
 +
}
 +
  .plasmid .noncodingregion {
 +
  fill: none;
 +
  stroke: #a3b6bb;
 +
  stroke-dasharray: 4,2;
 +
}
 +
  .plasmid .noncodinglabel {
 +
  font: 400 9px "Quicksand";
 +
  fill: #5e7980;
 +
}
 +
  .plasmid .atracklabel {
 +
  font: 400 20px "Quicksand";
 +
  color: #5e7980;
 +
  text-anchor: middle;
 +
}
 +
  .plasmid .atracklabel h1 {
 +
  font: 700 40px "Quicksand";
 +
}
 +
  .plasmid .atracklabel .tiny {
 +
  font: 400 12px "Quicksand";
 +
  margin-top: 10px;
 
}
 
}
  
−
.BB-prefix, .BB-suffix { width:10%;background-color:#e7e6e6;}
+
.element_info_box_container {
−
.rbs {width:20%;background-color:#eaa1a8;}
+
width:95%;
−
.yncm {width:25%; background-color:#fadda2;}
+
height:460px;
−
.his {width:10%;background-color:#a396c6;}
+
overflow:scroll;
−
.tev {width:10%;background-color:#f1ccf0;}
+
background-color:#e2e2e2;
−
.winsulin {width:25%;background-color:#b0dfb3;}
+
border-radius:20px;
−
.divider {width:2%;
+
−
height:50px;
+
−
display:inline-block;
+
−
text-align: center;
+
−
vertical-align: middle;
+
−
line-height: 50px;
+
−
font-family:'Quicksand';
+
−
font-size: 3.75vw;  }
+
−
+
−
+
−
.construct {
+
−
width:100%;
+
−
display:flex;
+
−
flex-direction:row;
+
−
flex-wrap:nowrap;
+
−
justify-content:space-evenly
+
−
align-items:center;
+
−
align-content:stretch;
+
 
}
 
}
 +
.pus270_container {
 +
display:flex;
 +
flex-direction:row;
 +
flex-wrap: nowrap ;
 +
justify-content:  space-around;
 +
align-items:center;
 +
align-content:space-around;
 +
}
 +
.pus_270 {flex-basis:60%;}
 +
.pus_270_info {flex-grow:2;}
  
−
 
+
.lacr_info, .pip_info, .eoriv_info, .mcs_info, .anti_info, .boriv_info, .laco_info, .super_info {display:none;}
 
</style>
 
</style>
 +
 
</head>
 
</head>
 
<body>
 
<body>
  
−
<div class="row" style="margin-top:150px;margin-left:10%;margin-right:10%">
+
<div class="pus270_container">
 +
<div class="pus_270">
 +
<plasmid id="pdemo" class="plasmid" plasmidheight="450" plasmidwidth="600" sequencelength="1240">
 +
    <plasmidtrack style="fill:#e2e2e2;stroke:none;" trackclass="track" radius="200" width="5">
 +
    <!-- plasmid title -->
 +
        <tracklabel text="pUS270" labelstyle="font-size:30px;font-weight:700;font-family:'Quicksand';"></tracklabel>
 +
        <tracklabel text="5707 bp" labelstyle="font-size:18px;font-weight:400;font-family:'Quicksand';" vadjust="25"></tracklabel>
  
−
<div class="construct">
+
 
−
<div class="BB-prefix element">
+
        <!-- NeoR/KanR -->   
−
BB prefix
+
  <trackmarker markerclass="markerhover" start="0" end="200" style="fill:#f2cbf1"  arrowendlength="15" arrowendwidth="10" vadjust="-10" wadjust="20">
 +
                <svgelement type="a" xlink:href="" id="anti" target="_blank">
 +
            <markerlabel labelclass="markerlabel" text="NeoR/KanR" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
 
 +
  </trackmarker>
 +
        <!-- pIP501 Rep -->   
 +
  <trackmarker markerclass="markerhover" start="220" end="420" style="fill:#b1d7dd" arrowendlength="15" arrowendwidth="10" vadjust="-10" wadjust="20">
 +
                <svgelement type="a" xlink:href="" id="pip" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="pIP501 Rep" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
      <!-- B. Subtilis OriV -->   
 +
  <trackmarker markerclass="markerhover" start="440" end="540" style="fill:#eca0a7" vadjust="-10" wadjust="20">
 +
                    <svgelement type="a" xlink:href="" id="boriv" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="B. Subtilis OriV" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
 
 +
        <!-- E. Coli OriV -->   
 +
  <trackmarker markerclass="markerhover" start="560" end="660" style="fill:#fbde9e" vadjust="-10" wadjust="20">
 +
                    <svgelement type="a" xlink:href="" id="eoriv" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="E. Coli OriV" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
 +
        <!-- Lac Operator -->   
 +
  <trackmarker markerclass="markerhover" start="680" end="780" style="fill:#cdf8ff" vadjust="-10" wadjust="20">
 +
                    <svgelement type="a" xlink:href="" id="laco" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="Lac Operator" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
 
 +
        <!-- MCS -->   
 +
  <trackmarker markerclass="markerhover" start="800" end="840" style="fill:#d0cece" vadjust="-10" wadjust="20">
 +
                  <svgelement type="a" xlink:href="" id="mcs1" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="MCS" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
      <!-- Sf-AmilCP-6 -->   
 +
  <trackmarker markerclass="markerhover" start="860" end="1000" style="fill:#a395c8" arrowendlength="15" arrowendwidth="10" vadjust="-10" wadjust="20">
 +
                  <svgelement type="a" xlink:href="" id="super" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="Sf-AmilCP-6" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
 +
 
 +
      <!-- MCS -->   
 +
  <trackmarker markerclass="markerhover" start="1020" end="1060" style="fill:#d0cece" vadjust="-10" wadjust="20">
 +
                  <svgelement type="a" xlink:href="" id="mcs2" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="MCS" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
 
 +
      <!-- LacI-->   
 +
  <trackmarker markerclass="markerhover" start="1080" end="1220" style="fill:#afe0b2" arrowendlength="15" arrowendwidth="10" vadjust="-10" wadjust="20">
 +
                    <svgelement type="a" xlink:href="" id="lacr" target="_blank">
 +
          <markerlabel labelclass="markerlabel" text="LacI" style="fill:#3e3f3f;font-weight:700;font-family:'Quicksand';font-size:16px;" ></markerlabel>
 +
            </svgelement>
 +
            </trackmarker>
 +
 +
    </plasmidtrack>
 +
</plasmid>
 
</div>
 
</div>
−
<div class="divider"></div>
+
<div class="pus_270_info element_info_box_container">
−
<div class="rbs element">RBS
+
<div class="lacr_info">
 +
<h6>Lac Operon Repressor</h6>
 +
 
 +
<h4>Codes for the production of the repressor protein that binds to the Lac Operator to prevent expression until induction of the media with IPTG. We have designed pUS270 to have the LacI under the pVeg promoter for strong constitutive expression in Bacillus.</h4>
 
</div>
 
</div>
−
<div class="divider"></div>
+
 
−
<div class="yncm element">
+
<div class="pip_info">
−
YNCM Tag
+
<h6>pIP501 Rep</h6>
 +
<h4>This gene codes for the Replicator protein that pairs with the Bacillus OriV and is essential to promote the independent replication of pUS270 in Bacillus. </h4>
 
</div>
 
</div>
−
<div class="yncm-arrow arrow-right"></div>
+
 
−
<div class="divider"></div>
+
<div class="eoriv_info">
−
<div class="his element">
+
<h6>E. coli OriV</h6>
−
His Tag
+
<h4>Taken from pSB1C3, having this origin of replication will make it easier to construct the plasmid using E. coli as well as improve cloning efficiency downstream. Chosen because of the high copy number of pSB1C3.</h4>
 
</div>
 
</div>
−
<div class="his-arrow arrow-right"></div>
+
 
−
<div class="divider"></div>
+
<div class="mcs_info">
−
<div class="tev element">
+
<h6>Multiple Cloning Site</h6>
−
TEV
+
<h4>The multiple cloning site of pUS258 and other expression plasmids that we considered using either had too few restriction sites or sites that were incompatible for the efficient cloning with the BB Prefix and Suffix. So we have designed two highly diverse MCS’ that have 27 unique sites amongst them on either side of SF AmylCP-6 to promote simple cloning of parts from the Bio Brick Registry.</h4>
 
</div>
 
</div>
−
<div class="tev-arrow arrow-right"></div>
+
 
−
<div class="divider"></div>
+
<div class="anti_info">
−
<div class="winsulin element">
+
<h6>Antibiotic Resistance</h6>
−
Winsulin
+
 
 +
<h4>Codes for Neomycin Phosphotransferase II that gives transformants resistance to both Neomycin and Kanamycin. Allows selective screening of transformants</h4>
 
</div>
 
</div>
−
<div class="winsulin-arrow arrow-right"></div>
+
 
−
<div class="divider"></div>
+
<div class="boriv_info">
−
<div class="BB-suffix element">
+
<h6> Antibiotic Resistance </h6>
−
BB suffix
+
<h4>This region allows independent replication of the vector within Bacillus at a high copy number to provide more copies of the recombinant gene to maximise expression.</h4>
 
</div>
 
</div>
−
<div class="arrow-right"></div>
+
 
 +
<div class="laco_info">
 +
<h6>Lac Operator </h6>
 +
<h4>Consists of the target sequence for the lac repressor protein to contribute to the IPTG induction system.</h4>
 
</div>
 
</div>
 +
 +
<div class="super_info">
 +
<h6>SuperFold AmilCP-6</h6>
 +
<h4>SuperFold AmilCP-6 is a variant of amilCP which was used by the 2016 Sydney IGEM team and originally submitted to the registry by Team Uppsala Sweden in 2011. This variant has undergone site directed mutagenesis to increase the folding rate of the chromoprotein and enhance the blue colour. We are taking advantage of this protein to enable blue-white screening without the need for adding X-gal to the plates. Cloning with the two multiple cloning sites that flank SF AmilCP-6 essentially swaps it with the insert to leave the recombinant bacteria white rather than blue. </h4>
 
</div>
 
</div>
 +
 +
 +
 
</div>
 
</div>
 +
</div>
 +
 
</body>
 
</body>
 
</html>
 
</html>
 +
 +
 
 +
        <!-- RECTANGLE -->
 +
        <trackmarker markerclass="markerhover" style="fill:rgba(0,0,128,.4)" start="482" end="567" wadjust="8" vadjust="-4" markerclick="markerClick($event, $marker)">
 +
            <markerlabel labelclass="markerlabel" text="LEUII" style="fill:#fff;font-weight:700" ></markerlabel>
 +
        </trackmarker>

Latest revision as of 10:43, 1 November 2017

Lac Operon Repressor

Codes for the production of the repressor protein that binds to the Lac Operator to prevent expression until induction of the media with IPTG. We have designed pUS270 to have the LacI under the pVeg promoter for strong constitutive expression in Bacillus.

pIP501 Rep

This gene codes for the Replicator protein that pairs with the Bacillus OriV and is essential to promote the independent replication of pUS270 in Bacillus.

E. coli OriV

Taken from pSB1C3, having this origin of replication will make it easier to construct the plasmid using E. coli as well as improve cloning efficiency downstream. Chosen because of the high copy number of pSB1C3.

Multiple Cloning Site

The multiple cloning site of pUS258 and other expression plasmids that we considered using either had too few restriction sites or sites that were incompatible for the efficient cloning with the BB Prefix and Suffix. So we have designed two highly diverse MCS’ that have 27 unique sites amongst them on either side of SF AmylCP-6 to promote simple cloning of parts from the Bio Brick Registry.

Antibiotic Resistance

Codes for Neomycin Phosphotransferase II that gives transformants resistance to both Neomycin and Kanamycin. Allows selective screening of transformants

Antibiotic Resistance

This region allows independent replication of the vector within Bacillus at a high copy number to provide more copies of the recombinant gene to maximise expression.

Lac Operator

Consists of the target sequence for the lac repressor protein to contribute to the IPTG induction system.

SuperFold AmilCP-6

SuperFold AmilCP-6 is a variant of amilCP which was used by the 2016 Sydney IGEM team and originally submitted to the registry by Team Uppsala Sweden in 2011. This variant has undergone site directed mutagenesis to increase the folding rate of the chromoprotein and enhance the blue colour. We are taking advantage of this protein to enable blue-white screening without the need for adding X-gal to the plates. Cloning with the two multiple cloning sites that flank SF AmilCP-6 essentially swaps it with the insert to leave the recombinant bacteria white rather than blue. 


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